import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
/**
 * Shared types for MAF alignment data
 */
/**
 * Options for MAF adapter getFeatures call.
 * Extends BaseOptions with optional samples filter for subtree optimization.
 */
export interface MafAdapterOptions extends BaseOptions {
    /** If provided, only parse alignments for these sample IDs */
    samples?: Sample[];
}
/**
 * Represents a single organism's alignment within a MAF block.
 * Used by adapters to return alignment data and by rendering code.
 */
export interface AlignmentRecord {
    /** Chromosome/contig name */
    chr: string;
    /** Start position in the organism's coordinate system */
    start: number;
    /** Total size of the source sequence (optional - not used in rendering) */
    srcSize?: number;
    /** Strand: 1 for forward, -1 for reverse (optional - not used in rendering) */
    strand?: number;
    /** Unknown field from MAF format (optional) */
    unknown?: number;
    /** The aligned sequence (including gaps as '-') */
    seq: string;
}
/**
 * A MAF feature containing alignments from multiple organisms
 */
export interface MafFeature {
    start: number;
    end: number;
    refName: string;
    /** Reference sequence */
    seq: string;
    /** Map of organism ID to alignment record */
    alignments: Record<string, AlignmentRecord>;
}
/**
 * Sample/organism metadata for display
 */
export interface Sample {
    id: string;
    label?: string;
    color?: string;
}
/**
 * Genomic region for queries and rendering
 */
export interface GenomicRegion {
    start: number;
    end: number;
    refName: string;
}